Not-from-concentrate (NFC) juice effectively retains the original characteristics of the fruit. Despite the various health benefits of Goji berries, reports on the processing technology and quality changes of NFC goji juice are lacking. We optimised the processing technology of NFC goji juice. Employing fuzzy mathematics evaluation combined with response surface methodology based on single-factor experiments, the physicochemical, nutritional, and microbiological indicators of the juice were determined. Gas chromatography-ion mobility spectroscopy was used to analyse changes in volatile compounds before and after processing. The optimal processing parameters were: times for homogenisation, ultrasonication, and sterilisation of 2 min, 3 min, and 85 s, respectively, and sterilisation temperature of 102 °C. The resulting product had a sensory evaluation score of 85.5 and a rich, pleasant taste. The ratio of total soluble solids to titratable acidity and turbidity were 12.8 and 1420 NTU, respectively. Post-processing, the contents of β-carotene, polysaccharides, and betaine increased by 57.3%, 26.7%, and 31.5%, respectively. Microbiological indicators met Chinese national limits for food pollutants and microorganisms. The total relative content of volatile substances in NFC goji juice decreased by 19.86% after processing. This study provides a theoretical reference for the intensive processing and development of high-value goji berries.